ZBP1

Last updated

ZBP1
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases ZBP1 , C20orf183, DAI, DLM-1, DLM1, Z-DNA binding protein 1
External IDs OMIM: 606750; MGI: 1927449; HomoloGene: 10972; GeneCards: ZBP1; OMA:ZBP1 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

81030

58203

Ensembl

ENSG00000124256

ENSMUSG00000027514

UniProt

Q9H171

Q9QY24

RefSeq (mRNA)

NM_001160417
NM_001160418
NM_001160419
NM_030776
NM_001323966

Contents

NM_001139519
NM_021394

RefSeq (protein)

NP_001153889
NP_001153890
NP_001153891
NP_001310895
NP_110403

NP_001132991
NP_067369

Location (UCSC) Chr 20: 57.6 – 57.62 Mb Chr 2: 173.05 – 173.06 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Z-DNA-binding protein 1, also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1, is a protein that in humans is encoded by the ZBP1 gene. [5] [6]

ZBP1 is also an abbreviation for chicken or rat β-actin zipcode-binding protein 1, a homolog of the human insulin-like growth factor 2 mRNA-binding protein 1 (IMP-1) and murine CRD-BP, the proteins involved in mRNA transport (RNA-binding proteins, RBPs).

History

ZBP1 was first identified as an interferon-inducible Z-NA binding protein, [7] but its specific functions remained unclear for many years. It was initially thought to be a cytosolic DNA sensor. However, the generation of Zbp1-deficient mice revealed that these mice responded normally to DNA and DNA virus infections, producing normal levels of interferon. [8]

Further insights came with the discovery of ZBP1's receptor-interacting protein homotypic interaction motif (RHIM) domains, which mediate interactions with other proteins. Experiments showed that ZBP1 interacts with RIPK1 and RIPK3 through these RHIM domains. [9] This interaction hinted at ZBP1's involvement in cell death, especially given the role of RIPK proteins in cell death pathways.

The role of ZBP1 as an innate immune sensor became more evident with the discovery that it regulates NLRP3 inflammasome activation and inflammatory cell death, PANoptosis, during influenza A virus infection. ZBP1-deficient mice showed impaired activation of inflammasome components, such as caspase-1, and reduced levels of IL-1β and IL-18, highlighting its critical role in antiviral defense. [10]

Structure

ZBP1 has several key domains that contribute to its function. At the N-terminus, it has Z-nucleic acid (Z-NA) binding domains, known as Zα1 and Zα2. Both Zα domains have a winged helix-turn-helix structure which allows them to bind to Z-RNA/DNA. [11] The intermediate region of ZBP1 contains two receptor-interacting protein homotypic interaction motif (RHIM) domains, RHIM1 and RHIM2, which facilitate interactions with other RHIM domain-containing proteins. [9] [12] [13] [14] The C-terminal region of ZBP1 contains a signal domain (SD), which is crucial for triggering an interferon response. [15] [16] [17] [18] [19]

Function and role in disease

ZBP1 was discovered as an innate immune sensor of influenza A virus that forms the ZBP1-PANoptosome to activate the NLRP3 inflammasome and drive cell death, PANoptosis. PANoptosis is a prominent innate immune, inflammatory, and lytic cell death pathway initiated by innate immune sensors and driven by caspases and receptor-interacting protein kinases (RIPKs) through PANoptosomes. [20] PANoptosomes are multi-protein complexes assembled by germline-encoded pattern-recognition receptor(s) (PRRs) (innate immune sensor(s)) in response to pathogens, including bacterial, viral, and fungal infections, as well as pathogen-associated molecular patterns, damage-associated molecular patterns, cytokines, and homeostatic changes during infections, inflammatory conditions, and cancer. [21] [22] [23] [24] Following the discoveries with IAV, the ZBP1-PANoptosome was also found to play a role in pathogenic inflammation in response to IFN therapy during coronavirus infection. [25]

In contrast, the ZBP1-PANoptosome can have therapeutic benefit in murine tumor models, where IFN and nuclear export inhibitor treatment modulates the ZBP1-ADAR1 pathway and drives ZBP1-PANoptosome formation to regress tumors. Recent research has identified curaxin (CBL0137), a small molecule inhibitor, to effectively induce ZBP1-mediated cell death in cancer-associated fibroblasts and effectively reverse immune checkpoint blockade (ICB) resistance in mouse models of melanoma. [26]

ZBP1 is also a key component of the absent in melanoma 2 (AIM2)-PANoptosome, which includes the AIM2 inflammasome, and assembles in response to Francisella novicida and herpes simplex virus 1 (HSV1) infections. [27] ZBP1 has also been extensively implicated in other viral infections, including coronaviruses, cytomegalovirus (CMV), [28] vaccinia (VACV), [29] varicella-zoster virus, [30] zika virus (ZIKV), [31] and others. Furthermore, ZBP1 also induces PANoptosis during Candida albicans and Aspergillus fumigatus infections. [32]

Z-NA binding

ZBP1 is proposed to be a Z-DNA binding protein. Z-DNA formation is a dynamic process, largely controlled by the amount of supercoiling. [6] ZBP1 recognizes DNA in the cytoplasm as an antiviral mechanism. Viral life cycles often include steps where DNA is exposed in the cytoplasm. DNA is normally contained in the nucleus of a cell, and therefore cells use proteins like ZBP1 as an indicator of a viral infection. Once ZBP1 is activated, it increases the production of antiviral cytokines such as interferon beta. [33] DLM1 then binds to cytosolic Viral DNA using two Z-DNA-binding domains (Zα and Zβ) at its N-terminus along with a DNA binding domain (D3). [34]

The role of ZBP1 in DNA sensing has been questioned. It has been found to sense Influenza A Virus (IAV) infection and induce cell death. Since DNA is not synthesized in any stage of IAV life cycle, DNA sensing playing a role in this context is unlikely. [35] [36] However, recent investigation has found that ZBP1 is capable of sensing Z-form RNAs produced during IAV infection, cumulating in a form of caspase independent, inflammatory cell death called necroptosis. [37]

A follow-up study identified that ZBP1 senses the IAV ribonucleoprotein complex to induce cell death. [36] A more recent study has identified transcription factor IRF1 as the upstream regulator of ZBP1 expression. [38]

Related Research Articles

<span class="mw-page-title-main">Caspase</span> Family of cysteine proteases

Caspases are a family of protease enzymes playing essential roles in programmed cell death. They are named caspases due to their specific cysteine protease activity – a cysteine in its active site nucleophilically attacks and cleaves a target protein only after an aspartic acid residue. As of 2009, there are 12 confirmed caspases in humans and 10 in mice, carrying out a variety of cellular functions.

Pattern recognition receptors (PRRs) play a crucial role in the proper function of the innate immune system. PRRs are germline-encoded host sensors, which detect molecules typical for the pathogens. They are proteins expressed mainly by cells of the innate immune system, such as dendritic cells, macrophages, monocytes, neutrophils, as well as by epithelial cells, to identify two classes of molecules: pathogen-associated molecular patterns (PAMPs), which are associated with microbial pathogens, and damage-associated molecular patterns (DAMPs), which are associated with components of host's cells that are released during cell damage or death. They are also called primitive pattern recognition receptors because they evolved before other parts of the immune system, particularly before adaptive immunity. PRRs also mediate the initiation of antigen-specific adaptive immune response and release of inflammatory cytokines.

<span class="mw-page-title-main">Interleukin 1 beta</span> Mammalian protein found in Homo sapiens

Interleukin-1 beta (IL-1β) also known as leukocytic pyrogen, leukocytic endogenous mediator, mononuclear cell factor, lymphocyte activating factor and other names, is a cytokine protein that in humans is encoded by the IL1B gene. There are two genes for interleukin-1 (IL-1): IL-1 alpha and IL-1 beta. IL-1β precursor is cleaved by cytosolic caspase 1 to form mature IL-1β.

<span class="mw-page-title-main">Caspase 1</span> Enzyme found in humans

Caspase-1/Interleukin-1 converting enzyme (ICE) is an evolutionarily conserved enzyme that proteolytically cleaves other proteins, such as the precursors of the inflammatory cytokines interleukin 1β and interleukin 18 as well as the pyroptosis inducer Gasdermin D, into active mature peptides. It plays a central role in cell immunity as an inflammatory response initiator. Once activated through formation of an inflammasome complex, it initiates a proinflammatory response through the cleavage and thus activation of the two inflammatory cytokines, interleukin 1β (IL-1β) and interleukin 18 (IL-18) as well as pyroptosis, a programmed lytic cell death pathway, through cleavage of Gasdermin D. The two inflammatory cytokines activated by Caspase-1 are excreted from the cell to further induce the inflammatory response in neighboring cells.

<span class="mw-page-title-main">NLRP3</span> Human protein and coding gene

NLR family pyrin domain containing 3 (NLRP3), is a protein that in humans is encoded by the NLRP3 gene located on the long arm of chromosome 1.

Pyroptosis is a highly inflammatory form of lytic programmed cell death that occurs most frequently upon infection with intracellular pathogens and is likely to form part of the antimicrobial response. This process promotes the rapid clearance of various bacterial, viral, fungal and protozoan infections by removing intracellular replication niches and enhancing the host's defensive responses. Pyroptosis can take place in immune cells and is also reported to occur in keratinocytes and some epithelial cells.

<span class="mw-page-title-main">RIPK1</span> Enzyme found in humans

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions in a variety of cellular pathways related to both cell survival and death. In terms of cell death, RIPK1 plays a role in apoptosis, necroptosis, and PANoptosis Some of the cell survival pathways RIPK1 participates in include NF-κB, Akt, and JNK.

<span class="mw-page-title-main">NLRC4</span> Protein-coding gene in the species Homo sapiens

NLR family CARD domain-containing protein 4 is a protein that in humans is encoded by the NLRC4 gene.

<span class="mw-page-title-main">NLRP12</span> Protein-coding gene in the species Homo sapiens

Nucleotide-binding oligomerization domain-like receptor (NLR) pyrin domain (PYD)-containing protein 12 is a protein that in humans is encoded by the NLRP12 gene.

<span class="mw-page-title-main">AIM2</span> Protein-coding gene in the species Homo sapiens

Interferon-inducible protein AIM2 also known as absent in melanoma 2 or simply AIM2 is a protein that in humans is encoded by the AIM2 gene.

<span class="mw-page-title-main">NOD-like receptor</span> Class of proteins

The nucleotide-binding oligomerization domain-like receptors, or NOD-like receptors (NLRs), are intracellular sensors of pathogen-associated molecular patterns (PAMPs) that enter the cell via phagocytosis or pores, and damage-associated molecular patterns (DAMPs) that are associated with cell stress. They are types of pattern recognition receptors (PRRs), and play key roles in the regulation of innate immune response. NLRs can cooperate with toll-like receptors (TLRs) and regulate inflammatory and apoptotic response.

Damage-associated molecular patterns (DAMPs) are molecules within cells that are a component of the innate immune response released from damaged or dying cells due to trauma or an infection by a pathogen. They are also known as danger signals, and alarmins because they serve as warning signs to alert the organism to any damage or infection to its cells. DAMPs are endogenous danger signals that are discharged to the extracellular space in response to damage to the cell from mechanical trauma or a pathogen. Once a DAMP is released from the cell, it promotes a noninfectious inflammatory response by binding to a pattern recognition receptor (PRR). Inflammation is a key aspect of the innate immune response; it is used to help mitigate future damage to the organism by removing harmful invaders from the affected area and start the healing process. As an example, the cytokine IL-1α is a DAMP that originates within the nucleus of the cell which, once released to the extracellular space, binds to the PRR IL-1R, which in turn initiates an inflammatory response to the trauma or pathogen that initiated the release of IL-1α. In contrast to the noninfectious inflammatory response produced by DAMPs, pathogen-associated molecular patterns (PAMPs) initiate and perpetuate the infectious pathogen-induced inflammatory response. Many DAMPs are nuclear or cytosolic proteins with defined intracellular function that are released outside the cell following tissue injury. This displacement from the intracellular space to the extracellular space moves the DAMPs from a reducing to an oxidizing environment, causing their functional denaturation, resulting in their loss of function. Outside of the aforementioned nuclear and cytosolic DAMPs, there are other DAMPs originated from different sources, such as mitochondria, granules, the extracellular matrix, the endoplasmic reticulum, and the plasma membrane.

Inflammasomes are cytosolic multiprotein complexes of the innate immune system responsible for the activation of inflammatory responses and cell death. They are formed as a result of specific cytosolic pattern recognition receptors (PRRs) sensing microbe-derived pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs) from the host cell, or homeostatic disruptions. Activation and assembly of the inflammasome promotes the activation of caspase-1, which then proteolytically cleaves pro-inflammatory cytokines, interleukin 1β (IL-1β) and interleukin 18 (IL-18), as well as the pore-forming molecule gasdermin D (GSDMD). The N-terminal GSDMD fragment resulting from this cleavage induces a pro-inflammatory form of programmed cell death distinct from apoptosis, referred to as pyroptosis, which is responsible for the release of mature cytokines. Additionally, inflammasomes can act as integral components of larger cell death-inducing complexes called PANoptosomes, which drive another distinct form of pro-inflammatory cell death called PANoptosis.

<span class="mw-page-title-main">NLRC5</span> Protein-coding gene in the species Homo sapiens

NLRC5, short for NOD-like receptor family CARD domain containing 5, is an intracellular protein that plays a role in the immune system. NLRC5 is a pattern recognition receptor implicated in innate immunity to viruses potentially by regulating interferon activity. It also acts as an innate immune sensor to drive inflammatory cell death, PANoptosis. In humans, the NLRC5 protein is encoded by the NLRC5 gene. It has also been called NOD27, NOD4, and CLR16.1.

<span class="mw-page-title-main">NLRP11</span> Protein-coding gene in the species Homo sapiens

NOD-like receptor family pyrin domain containing 11 is a protein that in humans is encoded by the NLRP11 gene located on the long arm of human chromosome 19q13.42. NLRP11 belongs to the NALP subfamily, part of a large subfamily of CATERPILLER. It is also known as NALP11, PYPAF6, NOD17, PAN10, and CLR19.6

NLRP (Nucleotide-binding oligomerization domain, Leucine rich Repeat and Pyrin domain containing), also abbreviated as NALP, is a type of NOD-like receptor. NOD-like receptors are a type of pattern recognition receptor that are found in the cytosol of the cell, recognizing signals of antigens in the cell. NLRP proteins are part of the innate immune system and detect conserved pathogen characteristics, or pathogen-associated molecular patterns, such as such as peptidoglycan, which is found on some bacterial cells. It is thought that NLRP proteins sense danger signals linked to microbial products, initiating the processes associated with the activation of the inflammasome, including K+ efflux and caspase 1 activation. NLRPs are also known to be associated with a number of diseases. Research suggests NLRP proteins may be involved in combating retroviruses in gametes. As of now, there are at least 14 different known NLRP genes in humans, which are named NLRP1 through NLRP14. The genes translate into proteins with differing lengths of leucine-rich repeat domains.

Murine caspase-11, and its human homologs caspase-4 and caspase-5, are mammalian intracellular receptor proteases activated by TLR4 and TLR3 signaling during the innate immune response. Caspase-11, also termed the non-canonical inflammasome, is activated by TLR3/TLR4-TRIF signaling and directly binds cytosolic lipopolysaccharide (LPS), a major structural element of Gram-negative bacterial cell walls. Activation of caspase-11 by LPS is known to cause the activation of other caspase proteins, leading to septic shock, pyroptosis, and often organismal death.

Immunogenic cell death is any type of cell death eliciting an immune response. Both accidental cell death and regulated cell death can result in immune response. Immunogenic cell death contrasts to forms of cell death that do not elicit any response or even mediate immune tolerance.

Thirumala-Devi Kanneganti is an immunologist and is the Rose Marie Thomas Endowed Chair, Vice Chair of the Department of Immunology, and Member at St. Jude Children's Research Hospital. She is also Director of the Center of Excellence in Innate Immunity and Inflammation at St. Jude Children's Research Hospital. Her research interests include investigating fundamental mechanisms of innate immunity, including inflammasomes and inflammatory cell death, PANoptosis, in infectious and inflammatory disease and cancer.

PANoptosis is a prominent innate immune, inflammatory, and lytic cell death pathway initiated by innate immune sensors and driven by caspases and receptor-interacting protein kinases (RIPKs) through multiprotein PANoptosome complexes. The assembly of the PANoptosome cell death complex occurs in response to germline-encoded pattern-recognition receptors (PRRs) sensing pathogens, including bacterial, viral, and fungal infections, as well as pathogen-associated molecular patterns, damage-associated molecular patterns, and cytokines that are released during infections, inflammatory conditions, and cancer. Several PANoptosome complexes, such as the ZBP1-, AIM2-, RIPK1-, and NLRC5- and NLRP12-PANoptosomes, have been characterized so far.

References

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  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000027514 – Ensembl, May 2017
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  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ↑ Rothenburg S, Schwartz T, Koch-Nolte F, Haag F (February 2002). "Complex regulation of the human gene for the Z-DNA binding protein DLM-1". Nucleic Acids Research. 30 (4): 993–1000. doi:10.1093/nar/30.4.993. PMC   100341 . PMID   11842111.
  6. 1 2 "Entrez Gene: ZBP1 Z-DNA binding protein 1".
  7. ↑ Fu Y, Comella N, Tognazzi K, Brown LF, Dvorak HF, Kocher O (November 1999). "Cloning of DLM-1, a novel gene that is up-regulated in activated macrophages, using RNA differential display". Gene. 240 (1): 157–163. doi:10.1016/s0378-1119(99)00419-9. PMID   10564822.
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  9. 1 2 Kaiser WJ, Upton JW, Mocarski ES (November 2008). "Receptor-interacting protein homotypic interaction motif-dependent control of NF-kappa B activation via the DNA-dependent activator of IFN regulatory factors". Journal of Immunology. 181 (9): 6427–6434. doi:10.4049/jimmunol.181.9.6427. PMC   3104927 . PMID   18941233.
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  11. ↑ Maelfait J, Rehwinkel J (August 2023). "The Z-nucleic acid sensor ZBP1 in health and disease". The Journal of Experimental Medicine. 220 (8): e20221156. doi:10.1084/jem.20221156. PMC   10347765 . PMID   37450010.
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  18. ↑ Schwartz T, Behlke J, Lowenhaupt K, Heinemann U, Rich A (September 2001). "Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins". Nature Structural Biology. 8 (9) (published 2001-09-01): 761–765. doi:10.1038/nsb0901-761. PMID   11524677.
  19. ↑ Rothenburg S, Schwartz T, Koch-Nolte F, Haag F (February 2002). "Complex regulation of the human gene for the Z-DNA binding protein DLM-1". Nucleic Acids Research. 30 (4): 993–1000. doi:10.1093/nar/30.4.993. PMC   100341 . PMID   11842111.
  20. ↑ Pandeya A, Kanneganti TD (January 2024). "Therapeutic potential of PANoptosis: innate sensors, inflammasomes, and RIPKs in PANoptosomes". Trends in Molecular Medicine. 30 (1): 74–88. doi:10.1016/j.molmed.2023.10.001. PMC   10842719 . PMID   37977994.
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  31. ↑ Daniels BP, Kofman SB, Smith JR, Norris GT, Snyder AG, Kolb JP, et al. (January 2019). "The Nucleotide Sensor ZBP1 and Kinase RIPK3 Induce the Enzyme IRG1 to Promote an Antiviral Metabolic State in Neurons". Immunity. 50 (1): 64–76.e4. doi:10.1016/j.immuni.2018.11.017. PMC   6342485 . PMID   30635240.
  32. ↑ Banoth B, Tuladhar S, Karki R, Sharma BR, Briard B, Kesavardhana S, et al. (December 2020). "ZBP1 promotes fungi-induced inflammasome activation and pyroptosis, apoptosis, and necroptosis (PANoptosis)". The Journal of Biological Chemistry. 295 (52): 18276–18283. doi: 10.1074/jbc.RA120.015924 . PMC   7939383 . PMID   33109609.
  33. ↑ Rathinam VA, Fitzgerald KA (March 2011). "Innate immune sensing of DNA viruses". Virology. 411 (2): 153–162. doi:10.1016/j.virol.2011.02.003. PMC   3070751 . PMID   21334037.
  34. ↑ Ha SC, Kim D, Hwang HY, Rich A, Kim YG, Kim KK (December 2008). "The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA". Proceedings of the National Academy of Sciences of the United States of America. 105 (52): 20671–20676. Bibcode:2008PNAS..10520671H. doi: 10.1073/pnas.0810463106 . PMC   2634953 . PMID   19095800.
  35. ↑ Kuriakose T, Man SM, Malireddi RK, Karki R, Kesavardhana S, Place DE, et al. (August 2016). "ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways". Science Immunology. 1 (2): aag2045. doi:10.1126/sciimmunol.aag2045. PMC   5131924 . PMID   27917412.
  36. 1 2 Kesavardhana S, Kuriakose T, Guy CS, Samir P, Malireddi RK, Mishra A, et al. (August 2017). "ZBP1/DAI ubiquitination and sensing of influenza vRNPs activate programmed cell death". The Journal of Experimental Medicine. 214 (8): 2217–2229. doi:10.1084/jem.20170550. PMC   5551577 . PMID   28634194.
  37. ↑ Zhang T, Yin C, Boyd DF, Quarato G, Ingram JP, Shubina M, et al. (March 2020). "Influenza Virus Z-RNAs Induce ZBP1-Mediated Necroptosis". Cell. 180 (6): 1115–1129.e13. doi:10.1016/j.cell.2020.02.050. PMC   7153753 . PMID   32200799.
  38. ↑ Kuriakose T, Zheng M, Neale G, Kanneganti TD (February 2018). "IRF1 Is a Transcriptional Regulator of ZBP1 Promoting NLRP3 Inflammasome Activation and Cell Death during Influenza Virus Infection". Journal of Immunology. 200 (4): 1489–1495. doi:10.4049/jimmunol.1701538. PMC   6483084 . PMID   29321274.

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